A citation-based method for searching scientific literature

Mark J P Chaisson, Ashley D Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J Gardner, Oscar L Rodriguez, Li Guo, Ryan L Collins, Xian Fan, Jia Wen, Robert E Handsaker, Susan Fairley, Zev N Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M Wenger, Alex R Hastie, Danny Antaki, Thomas Anantharaman, Peter A Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T Chuang, Christine C Lambert, Deanna M Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David U Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Ernest T Lam, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Shantao Li, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M Munson, Fabio C P Navarro, Bradley J Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy W C Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian Stütz, Diana C J Spierings, Alistair Ward, AnneMarie E Welch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Ernesto Lowy, Sergei Yakneen, Steven McCarroll, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B Gerstein, Pui-Yan Kwok, Peter M Lansdorp, Gabor T Marth, Jonathan Sebat, Xinghua Shi, Ali Bashir, Kai Ye, Scott E Devine, Michael E Talkowski, Ryan E Mills, Tobias Marschall, Jan O Korbel, Evan E Eichler, Charles Lee. Nat Commun 2019
Times Cited: 213







List of co-cited articles
709 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


An integrated map of structural variation in 2,504 human genomes.
Peter H Sudmant, Tobias Rausch, Eugene J Gardner, Robert E Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz,[...]. Nature 2015
936
34


Characterizing the Major Structural Variant Alleles of the Human Genome.
Peter A Audano, Arvis Sulovari, Tina A Graves-Lindsay, Stuart Cantsilieris, Melanie Sorensen, AnneMarie E Welch, Max L Dougherty, Bradley J Nelson, Ankeeta Shah, Susan K Dutcher,[...]. Cell 2019
134
28

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
27

Accurate detection of complex structural variations using single-molecule sequencing.
Fritz J Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler, Michael C Schatz. Nat Methods 2018
340
25

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard J Hall, Gregory T Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson,[...]. Nat Biotechnol 2019
215
21

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
21

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.
Xiaoyu Chen, Ole Schulz-Trieglaff, Richard Shaw, Bret Barnes, Felix Schlesinger, Morten Källberg, Anthony J Cox, Semyon Kruglyak, Christopher T Saunders. Bioinformatics 2016
462
20

DELLY: structural variant discovery by integrated paired-end and split-read analysis.
Tobias Rausch, Thomas Zichner, Andreas Schlattl, Adrian M Stütz, Vladimir Benes, Jan O Korbel. Bioinformatics 2012
803
19

LUMPY: a probabilistic framework for structural variant discovery.
Ryan M Layer, Colby Chiang, Aaron R Quinlan, Ira M Hall. Genome Biol 2014
535
18

Nanopore sequencing and assembly of a human genome with ultra-long reads.
Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes,[...]. Nat Biotechnol 2018
596
18

Resolving the complexity of the human genome using single-molecule sequencing.
Mark J P Chaisson, John Huddleston, Megan Y Dennis, Peter H Sudmant, Maika Malig, Fereydoun Hormozdiari, Francesca Antonacci, Urvashi Surti, Richard Sandstrom, Matthew Boitano,[...]. Nature 2015
378
16

Telomere-to-telomere assembly of a complete human X chromosome.
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon,[...]. Nature 2020
116
16

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs.
Ashley D Sanders, Ester Falconer, Mark Hills, Diana C J Spierings, Peter M Lansdorp. Nat Protoc 2017
34
44

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.
Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy. Genome Res 2017
15

Discovery and genotyping of structural variation from long-read haploid genome sequence data.
John Huddleston, Mark J P Chaisson, Karyn Meltz Steinberg, Wes Warren, Kendra Hoekzema, David Gordon, Tina A Graves-Lindsay, Katherine M Munson, Zev N Kronenberg, Laura Vives,[...]. Genome Res 2017
148
15

Initial sequencing and analysis of the human genome.
E S Lander, L M Linton, B Birren, C Nusbaum, M C Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh,[...]. Nature 2001
15


The impact of structural variation on human gene expression.
Colby Chiang, Alexandra J Scott, Joe R Davis, Emily K Tsang, Xin Li, Yungil Kim, Tarik Hadzic, Farhan N Damani, Liron Ganel, Stephen B Montgomery,[...]. Nat Genet 2017
112
14

A robust benchmark for detection of germline large deletions and insertions.
Justin M Zook, Nancy F Hansen, Nathan D Olson, Lesley Chapman, James C Mullikin, Chunlin Xiao, Stephen Sherry, Sergey Koren, Adam M Phillippy, Paul C Boutros,[...]. Nat Biotechnol 2020
36
38

Genome maps across 26 human populations reveal population-specific patterns of structural variation.
Michal Levy-Sakin, Steven Pastor, Yulia Mostovoy, Le Li, Alden K Y Leung, Jennifer McCaffrey, Eleanor Young, Ernest T Lam, Alex R Hastie, Karen H Y Wong,[...]. Nat Commun 2019
45
28


Mapping and phasing of structural variation in patient genomes using nanopore sequencing.
Mircea Cretu Stancu, Markus J van Roosmalen, Ivo Renkens, Marleen M Nieboer, Sjors Middelkamp, Joep de Ligt, Giulia Pregno, Daniela Giachino, Giorgia Mandrile, Jose Espejo Valle-Inclan,[...]. Nat Commun 2017
126
13

Piercing the dark matter: bioinformatics of long-range sequencing and mapping.
Fritz J Sedlazeck, Hayan Lee, Charlotte A Darby, Michael C Schatz. Nat Rev Genet 2018
149
13

Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing.
Shunichi Kosugi, Yukihide Momozawa, Xiaoxi Liu, Chikashi Terao, Michiaki Kubo, Yoichiro Kamatani. Genome Biol 2019
89
14

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.
Ester Falconer, Mark Hills, Ulrike Naumann, Steven S S Poon, Elizabeth A Chavez, Ashley D Sanders, Yongjun Zhao, Martin Hirst, Peter M Lansdorp. Nat Methods 2012
77
15

Phased diploid genome assembly with single-molecule real-time sequencing.
Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz,[...]. Nat Methods 2016
628
12

A structural variation reference for medical and population genetics.
Ryan L Collins, Harrison Brand, Konrad J Karczewski, Xuefang Zhao, Jessica Alföldi, Laurent C Francioli, Amit V Khera, Chelsea Lowther, Laura D Gauthier, Harold Wang,[...]. Nature 2020
106
12

Structural variant calling: the long and the short of it.
Medhat Mahmoud, Nastassia Gobet, Diana Ivette Cruz-Dávalos, Ninon Mounier, Christophe Dessimoz, Fritz J Sedlazeck. Genome Biol 2019
56
21

Characterizing polymorphic inversions in human genomes by single-cell sequencing.
Ashley D Sanders, Mark Hills, David Porubský, Victor Guryev, Ester Falconer, Peter M Lansdorp. Genome Res 2016
37
29

Genome structural variation discovery and genotyping.
Can Alkan, Bradley P Coe, Evan E Eichler. Nat Rev Genet 2011
736
11

De novo assembly and phasing of a Korean human genome.
Jeong-Sun Seo, Arang Rhie, Junsoo Kim, Sangjin Lee, Min-Hwan Sohn, Chang-Uk Kim, Alex Hastie, Han Cao, Ji-Young Yun, Jihye Kim,[...]. Nature 2016
167
11

Integrative detection and analysis of structural variation in cancer genomes.
Jesse R Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria T Le, Galip Gürkan Yardımcı, Abhijit Chakraborty, Darrin V Bann, Yanli Wang,[...]. Nat Genet 2018
97
11

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.
Ernest T Lam, Alex Hastie, Chin Lin, Dean Ehrlich, Somes K Das, Michael D Austin, Paru Deshpande, Han Cao, Niranjan Nagarajan, Ming Xiao,[...]. Nat Biotechnol 2012
311
11

Integrative genomics viewer.
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz, Jill P Mesirov. Nat Biotechnol 2011
11


Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Peter Ebert, Peter A Audano, Qihui Zhu, Bernardo Rodriguez-Martin, David Porubsky, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari,[...]. Science 2021
22
50

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.
Grace X Y Zheng, Billy T Lau, Michael Schnall-Levin, Mirna Jarosz, John M Bell, Christopher M Hindson, Sofia Kyriazopoulou-Panagiotopoulou, Donald A Masquelier, Landon Merrill, Jessica M Terry,[...]. Nat Biotechnol 2016
302
10

Dense and accurate whole-chromosome haplotyping of individual genomes.
David Porubsky, Shilpa Garg, Ashley D Sanders, Jan O Korbel, Victor Guryev, Peter M Lansdorp, Tobias Marschall. Nat Commun 2017
42
23


Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis.
Hayk Barseghyan, Wilson Tang, Richard T Wang, Miguel Almalvez, Eva Segura, Matthew S Bramble, Allen Lipson, Emilie D Douine, Hane Lee, Emmanuèle C Délot,[...]. Genome Med 2017
35
28

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
10

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.
Justin M Zook, Brad Chapman, Jason Wang, David Mittelman, Oliver Hofmann, Winston Hide, Marc Salit. Nat Biotechnol 2014
411
9

Phenotypic impact of genomic structural variation: insights from and for human disease.
Joachim Weischenfeldt, Orsolya Symmons, François Spitz, Jan O Korbel. Nat Rev Genet 2013
244
9

SVIM: structural variant identification using mapped long reads.
David Heller, Martin Vingron. Bioinformatics 2019
34
26

Long-read sequencing and de novo assembly of a Chinese genome.
Lingling Shi, Yunfei Guo, Chengliang Dong, John Huddleston, Hui Yang, Xiaolu Han, Aisi Fu, Quan Li, Na Li, Siyi Gong,[...]. Nat Commun 2016
120
9

Long-read sequence and assembly of segmental duplications.
Mitchell R Vollger, Philip C Dishuck, Melanie Sorensen, AnneMarie E Welch, Vy Dang, Max L Dougherty, Tina A Graves-Lindsay, Richard K Wilson, Mark J P Chaisson, Evan E Eichler. Nat Methods 2019
47
19


Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome.
Wouter De Coster, Peter De Rijk, Arne De Roeck, Tim De Pooter, Svenn D'Hert, Mojca Strazisar, Kristel Sleegers, Christine Van Broeckhoven. Genome Res 2019
49
18

Direct determination of diploid genome sequences.
Neil I Weisenfeld, Vijay Kumar, Preyas Shah, Deanna M Church, David B Jaffe. Genome Res 2017
263
9


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.